Build Your Own Cladogram! In this activity, you will try to build a cladogram based on the morphology of given animals. Material: photos given in the procedure Procedure: 1.Your class will be divided into groups with 5 members each. 2.With the photos provided by your teacher in Fig.1, try to cut out the figure of each animal. 3.Lay out all animals on your desk and try to group the animals based on the presence or absence of the backbone. Build the initial segment of your phylogenetic tree as shown in the figure below. Place all the animals with a backbone at the end of the corresponding branch. Do the same for those with no backbone. 4.Think of other traits that you can separate the animals within the existing groups. 5.Make sure that you use different traits in order to separate and isolate animals into smaller and smaller groups. This will also expand your phylogenetic tree into several divisions. For example, you must think of a trait that can further subdivide the animals within the “backbone” branch into smaller groups. ○ Do this until each animal is positioned in its own branch. Once the animal is positioned on its own branch, paste it to the end of that branch on your tree. 6. Answer the guide questions afterward. Figure 1 Guide Questions: 1. Based on what you have learned in the previous unit, what is a phylogenetic tree? How is it different from a cladogram? 2. Based on the activity, what possible data can be used in constructing the phylogenetic tree or cladogram? 3. Where do you think you can use phylogenetic trees? 4. What do you think is the importance of phylogenetic trees in the field of taxonomy? 5. Do you think it is possible to build a phylogenetic tree of all organisms on the planet? Explain your answer. History of Taxonomy With the astounding diversity of creatures on Earth, we have to find ways to properly name them. Thus, taxonomy was established. Taxonomy (from ancient Greek words taxis, which means "arrangement," and nomia, which means "method") is a science that deals with the classification of organisms based on shared characteristics. This field is sometimes called systematics, or biosystematics. How are these organisms named or classified and why is it important to classifythem? _ _ _ _ _ _ _ _ _ Taxonomy is the science of classifying and naming organisms. Taxonomy classifies organisms based on their relatedness which is why phylogenetic trees are relevant in this field. At the same time, evolutionary relationships of organisms are also being considered to provide a more comprehensive understanding of the overall connection of one organism to another. In general, the field of taxonomy can be divided into three major functions. These are identification, naming, and classification. Identification and Description Taxonomy deals with the identification of organisms. To do this, modern-day taxonomists provide comprehensive taxonomic descriptions of all documented species on Earth. The taxonomic descriptions can be based on morphology, behavior, and genetic data. Sometimes, these can be accompanied by taxonomic line drawings of the species that show how it looks like. These descriptions can be used by other people to properly identify species they encountered or collected in the field. Newly-discovered species are usually only scientifically recognized once they are published in a peer-reviewed publication. This is an extremely important step done in the science of taxonomy. The publication will usually propose a scientific name and contain illustrations, drawings, and descriptions of the organism that is focused on. Naming Taxonomy also deals with the naming of species. This is particularly important for newly discovered species that require their own scientific names. The subfield of Taxonomy that deals with the proper naming of organisms refers to nomenclature. Nomenclature is a set of rules that are followed in properly naming organisms. This topic will be further discussed in the next lesson. Classification Taxonomy deals with the proper groupings of organisms based on their morphological, genetic, and evolutionary relatedness. This is usually done by studying the phylogeny of the organisms. The process of classifying organisms in a highly organized manner refers to Systematics. However, you must take note that systematics is a broader science compared to taxonomy. It normally involves a much wider scope compared to taxonomy. The figure shows the difference between taxonomy and systematics. While taxonomy concerns itself with naming, identification, and classification, systematics take these a step further by attempting to determine evolutionary relationships between organisms. Grouping organisms allows researchers to have an overview of the connection between species. This provides an idea of how organisms may interact with each other. For example, the phylogeny of SARS-CoV-2, which is the cause of the COVID-19 pandemic, allows researchers to track the possible origins and intermediate hosts of the virus. With this, the proper classification of organisms into their proper taxonomic group is one of the main concerns of taxonomists. Taxonomy is an old field of Science. It can be as old as the early languages used by mankind. Taxonomy has been an essential field that allowed early human civilizations to identify edible and poisonous plants and animals. In this section, you will learn the general history of the development of taxonomy as a science it is known today. Earliest Taxonomists One of the early written taxonomic accounts was written by Shen Nong, an emperor from ancient China. He is considered the father of Chinese medicine who documented and identified hundreds of medicinal herbs. In his work that can be translated as “Divine Husbandman's Materia Medica,” emperor Nong documented a total of 365 medicines from identified plants and animals. In the Middle East (1500 BC), early Egyptians created illustrations of medicinal plants that were hand-painted on the wall. These paintings provided a general overview of the early medicinal plants in Egypt. In the earliest captured evidence, “Ebers Papyrus”, a papyrus document, plants were identified by early Egyptians and documented their different medicinal properties. They even provided local names to allow Egyptian doctors to identify the species in the field. Greek and Roman Taxonomists Aristotle (384–322 BC) - Aristotle is considered as one of the formally trained taxonomists. He was able to classify several species of vertebrates and invertebrates which he categorized as organisms with blood and without blood, respectively. Moreover, he classified animals according to the manner of giving birth: animals with blood into live-bearing and egg-bearing. With this, Aristotle introduced the dichotomous concepts of taxonomy that classify organisms by type through binomial definition. The binomial definition means that organisms can be described based on two names, namely: genus and species epithet. Aristotle's idea of classification states that organisms must be named according to a family, where each member can be differentiated from one another using some unique characteristics. For example, he defined humans as "rational animals" due to their ability to think and decide on things. Aristotle summarized all of his works in early taxonomy in the History of Animals (Latin: Historia Animalium), where he classified organisms based on their similarities. He thinks that organisms can be categorized in a hierarchical manner. He further described this as the "ladder of nature" (Scala Naturae) where life forms can be ranked into an organized system. Theophrastus (370–285 BC) was one of the students of Aristotle and Plato. Theophrastus wrote early works on the classification of all known plants in his work, “De Historia Plantarum.” In this book, he described 48 species of plants that he grouped according to growth form. This book was used for taxonomic purposes during the Middle Ages in Europe. Dioscorides (40–90 AD) is a well-known greek physician who documented Roman and Greek medicinal plants. He summarized all of his works in a book, “De Materia Medica”, which describes around 600 species. In this book, he tried to classify plants based on their medicinal properties. This book was used in medicine until the 16th century. Plinius (23–79 AD), more famously known as Pliny the Elder, was a Roman army commander who wrote many books about giving Latin names to plants. In his only surviving work, “Naturalis Historia” that contains 160 volumes, he described plants and then provided them with Latin names. Until today, several of these names are still recognized. 16th Century Taxonomists Caesalpino (1519–1603) was an Italian scientist who is considered as the "the first taxonomist". He wrote “De Plantis,” a book containing 1 500 species of plants that were classified based on the growth habit, fruit, and seed form. Bauhin Brothers (1541–1631; 1560–1624) were Swiss taxonomists who wrote “Pinax Theatri Botanici” in 1623. This work tries to list a total of 6 000 species of organisms. The Bauhin brothers cleared the issue of synonyms in naming organisms, which was a great issue in taxonomy at that time. There were some species that are known to have several different names according to different books. Their work tried to fix this issue by recognizing the concept of genera and species as major taxonomic levels. John Ray (1627–1705) was an English naturalist who wrote several important books about taxonomy. He established the concept of species as the ultimate unit of taxonomy. He published a book, “Methodus Plantarum Nova”, where he tried to identify a total of 18 000 plant species based on a relatively narrow species concept. Joseph Pitton de Tournefort (1656–1708) was a French naturalist who constructed a botanical classification that was dominantly followed in plant taxonomy until the time of Carl Linnaeus. He published “Institutiones Rei Herbariae”, which contains around 9 000 species from a total of 698 genera. He tried to emphasize the classification of plants based on genera. Carolus Linnaeus Carolus Linnaeus (1707–1778) was a Swedish taxonomist who started the modern botanical and zoological taxonomy. His contributions to the field has earned him the moniker “Father of Taxonomy”. He wrote the “Species Plantarum” that was published until 1758. This contains the baseline of the rules for botanical nomenclature. Also, Linnaeus published “Systema Naturae” in 1758 that contains information for zoological nomenclature. These books tried to document thousands of plants and animal species and provided the foundation for modern-day botanical and zoological taxonomic standards in terms of naming organisms. In these books, Linnaeus introduced the binary form of giving scientific names to all species. For each organism, he tried to create a specific epithet that is used together with the genus name. This was later known as the binary nomenclature system for naming organisms. This form of naming species is intended for fieldwork and taxonomy education. The binary nomenclature system developed by Linnaeus revolutionized the way organisms are named. It provided a more organized form of naming that avoided synonyms for each species. Carolus Linnaeus introduced several concepts that tried to standardized classification systems in both plants and animals. For example, he introduced the classification of plants based on sexual parts of the flower. This has ended years of debate on the issue of whether plants had sexuality or not. His practical use of the binomial system and comprehensive observations convinced the scientific community at that time that a sexual system of plants exists. Moreover, Linnaeus’ works helped botany and zoology to be transformed into Scientia, which is a scientific body based on philosophy, order, and systems. Overall, Linnaeus established many of the rules taxonomists use today. The Concept of Taxa Linnaeus considered the taxon (plural, taxa) to be a unit for the classification of organisms. Each taxon, regardless of rank, describes a certain set of organisms that have been grouped together on the basis of their similarities. Note that the concept of evolutionary relationships was still not very well known during Linnaeus’ time, which was a century before Charles Darwin. This means that the organisms that were grouped together in the early Linnaean concepts of classification were purely based on physical characteristics. Today, however, most taxa are classified on the basis of evolutionary relationships. Taxonomic Ranks As was mentioned earlier, Linnaeus proposed a classification system based on a taxonomic hierarchy. Linnaeus’ proposed system has been modified by other scientists over the centuries, but the essence of this contribution still remains. Today, there are eight major taxonomic ranks, which are as follows: The (1) domain rank, which separates organisms into the three-domain system, includes the Eukarya, Bacteria, and Archaea. Kingdom refers to the broadest classification that follows domains. Plants, animals, and fungi are classified into their own kingdoms. Phylum refers to the rank that follows a kingdom. This refers to the broad classifications of organisms that share common characteristics. (4) Class, (5) order, (6) family, (7) genus, and (8) species, respectively, are all classified as the lower levels or ranks in the hierarchy after the phylum. For all known species, each taxon in the hierarchy corresponds to a specific given name that denotes its classification. As is seen in the photo in Figure 1 below, the names of the classification for a red fox from domain to species levels are Eukarya, Animalia, Chordata, Mammalia, Carnivora, Canidae, Vulpes, Vulpes vulpes, respectively. If you look at the classifications for the ranks of other similar organisms, you may notice that they may share similarities in the names for specific ranks. Comparing the taxon names of the fox to the lion shown in Table 1 below, you may notice that they have several similarities. Specifically, everything from Order Carnivora and above is the same. This means that foxes and lions are related to each other as close as the order level. Different ranks in the classification of lions Different ranks in the classification of clams Another organism, the giant clam, is shown in the table above. This organism is more distantly related to both the red fox and the lion, with the lowest rank similarity seen in the kingdom level of Animalia. Also, note that the higher levels in the taxonomic hierarchy, from domain to species, are arranged from most inclusive to most exclusive. The levels above the hierarchy are most inclusive because of the number levels below it, as well as the apparently greater number of organisms belonging to them. By contrast, ranks that are located at lower levels in the hierarchy tend to be more exclusive because of the relatively lower number of organisms they have. The Process of Classification Upon the discovery of potentially novel species, scientists follow specific steps in order to establish the identity and uniqueness of these newly-discovered or newly-identified organisms. These steps are performed in order to prevent confusion between similar species and to formally establish the natural existence of the organism for the scientific community Some of these steps performed in biological classification are the following: Comparison and description. After the specimen has been obtained and prepared, descriptions of the characteristics, such as the morphological and anatomical features of the organism, must be done. These will then be compared with the characteristics of similar organisms in order to determine if the new organism is indeed unique. Molecular evidence analysis. This can also be done concurrently with comparison and description. Molecular evidence, such as DNA sequences, are used to determine whether the organism is indeed novel. Naming. If the organism is new to science, then it will be given a formal scientific name based on international standards. These standards vary based on whether the organism is an animal, plant, or another life form. This will be discussed in further detail later on. Classification. The novel species will then be classified into existing ranks or be given a new one based on uniqueness. The evolutionary history of the organism will also be determined in order to generate a more accurate classification. Importance of Naming Organisms In Filipino, a dog is called aso. In other countries, it is called inu (Japanese), gae (Korean), Chien (French), and anjing (Malaysia), to name a few. The word "dog" can be translated into over 80 different languages around the world. In this example, note that a single species, the dog, can be called using different names. Without a specific or unique name for that species, it is impossible to have a proper reference for that specific organism. By creating a system of naming organisms, confusion can be avoided. Common names vary among languages and even regions within a single country. The animal shown below can be called a cougar, a puma, a panther, or a mountain lion. To avoid confusion, scientists use the scientific name Puma concolor for this species. The scientific name uses Latin and Greek words, the languages understood by 18thcentury scientists. This practice is still followed today in naming newly discovered species, such as the Apomys brownorum, a newly discovered rodent species discovered in Luzon. Binomial Nomenclature Linnaeus is perhaps best-known for his proposal and use of the binomial nomenclature system. As the name implies, the binomial nomenclature system uses two names to refer to a species. Each species has its own unique binomial name. This means that a binomial name (commonly also referred to today as the scientific name) will only refer to one species and that species alone. Format A binomial name is made up of two words, which include the genus name and the specific epithet. These two, when used together, refer to a distinct species. Examples can be seen in Table 3 below: Examples of genus names and specific epithets for selected species Creating a binomial name is as simple as stringing together the genus name and the specific epithet. There are certain formatting guidelines to be followed, however. Some of these guidelines are the following: The first letter of the genus name should be capitalized. The first letter of the specific epithet should not be capitalized. When encoded digitally, the binomial name must be italicized. Example: Orcinus orca When written down manually, the binomial name must be underlined separately. Space must not be underlined. Example: Orcinus orca Name Origins The names for both genus and specific epithet are usually derived from Latin. This is because Latin is a dead language, which means that the definitions of its words are now unchanging. This is in contrast with modern languages, whose words still evolve to have new definitions. The use of a dead language ensures that the descriptions used in a scientific name are still applicable even as time passes. An example of these words can be seen below in the table below. Aside from using words that describe the organism, sometimes, the scientific name may be based on the place or locality where the organism can be found or a person who has made a significant contribution to its discovery. An example of a scientific name being named after a person was given in the table above. On the other hand, an example of a scientific name being named after a place is Naja philippinensis or the Philippine cobra, which is native to Luzon. Authority A scientific name, when used in publications, should include the authority of the name on its first mention. The authority of a name refers to the person who first used the scientific name. The way of writing these may vary based on whether the organism is an animal, plant, or another life form. Examples can be seen below. Plant: Arum maculatum L. ○ The “L.” in this case stands for “Linnaeus.” Animal: Panthera leo (Linnaeus, 1758) The surname of the author and the year of description must be added in parentheses after the binomial name. There are also several governing conventions that establish the rules on the naming of organisms and the use of scientific names. Some of these include: The International Code of Zoological Nomenclature, which is abbreviated as ICZN, governs the naming of animals. The International Code of Nomenclature for Algae, Fungi, and Plants, which is abbreviated as ICN, governs the naming of the groups mentioned. The Importance of the Linnaean System Classifying organisms into hierarchical ranks and giving them binomial names have several benefits. Some of these include uniqueness, uniformity, and organization. Because of the contributions of taxonomists, many organisms can now be classified based on different characteristics. Taxonomy has classified organisms into groups that have biological meaning. This modern way of classifying helps scientists study different organisms easily. Also, our goal to protect and conserve different species of organisms can be achieved because we can easily identify the species that are threatened and endangered. At present, different characteristics are used to classify and name organisms. Some of these include form, color, size, chemical structure, and even genetic makeup. Earlier attempts in classifying organisms used general appearances such as anatomical and physiological characteristics. However, the most recent ways of classifying and naming organisms focus more on genetic and molecular similarities. The arrival of modern technology has helped scientists provide better ways of classifying organisms. Uniqueness of the Name All binomial names are unique. This means that a scientific name can refer to one species of organisms and that species only. This can prevent confusion when referring to different species of organisms. Uniformity The use of a binomial name is universal. This means that the binomial name is used by the scientific community all around the world. This can prevent confusion because species names tend to have local variations depending on the area. For example, what we know as the maya in the Philippines are known as sparrows in English-speaking countries. These, however, are known as gorrión in Spanish-speaking localities and suzume in Japan. The term “sparrow” can also refer to a variety of similar birds of different species. The accepted common name for the mayas we know in the Philippines is the Eurasian tree sparrow. Therefore, to prevent confusion stemming from the use of all these names, the binomial name Passer montanus would be better. This binomial name, like all scientific names, is recognized internationally and is not shared by any other species. Organization The use of ranks also provides organization regarding the relationship between organisms. Looking at the respective hierarchical ranks can provide an indication of how closely-related or distantly-related organisms are from each other. SPECIES DIVERSITY In general, diversity refers to the degree of variation among living organisms. Diversity is usually measured in a variety of ways. Its measurement can start from variations in species and range to differences in ecosystem structure. The primary focus of this lesson is the variation within the species level. Particularly, this lesson highlights the degree of diversity within species and between species to know relatedness among organisms. Species diversity refers to the degree of variation among species in a given ecosystem. For example, a drop of pond water can be considered rich in species diversity because it tends to harbor a high diversity of protozoans, bacteria, phytoplankton, and zooplankton species. To simplify, species diversity tends to increase with the presence of a greater number of individuals that belong to different taxonomic groups. The measurement of species diversity is an important indicator of the current environmental health status of an ecosystem. A healthy ecosystem can sustain a more diverse group of species as it can provide a wide variety of resources needed by the different taxa. Conversely, a high species diversity may sometimes be indicative of a healthy ecosystem. Measurement of Species Diversity For ecologists, there are several ways of measuring species diversity in an ecosystem. This section aims to enumerate the common measurements that are used in order to estimate the diversity of species in a given type of ecosystem. Species Richness Species richness refers to the number of unique species present in a specific area. This measurement answers the question of how many distinct species are present within a specified area. To fully understand the concept of species richness, you may use the figure below. An example of an application of this is if a person is interested in knowing the degree of species richness within a coastal area in Mindoro Island. Measuring this will require a count of the total number of all species in that coastal area. Species will be counted regardless of whether they are plants, animals, or fungi. Species Abundance Another important concept of species diversity is the measurement of abundance. Species abundance refers to the total number of individuals that belong to one distinct species. With this, knowing the species abundance requires counting of the number of individuals per species that is present in a specific area. To contrast this with species richness, abundance counts the individuals per species in the area while richness counts the number of distinct species within the area. For example, the figure shows a species richness of 5 for the entire area because there is a total number of five species present. However, measuring the species abundance will require a count of the number of individuals present for each of these five species. Species Evenness Species evenness measures the diversity of species while considering the abundance of each species within the ecosystem. This is a measure of how close the abundances of species are in a given environment. Therefore, an area that has species with relatively close or equal abundance values will also have high species evenness. On the other end, if an area has abundance values that are very different across species, then species evenness will also be low. For example, two communities of trees are shown in the figure below. In comparing the species evenness of the two, one can say that community one is more even due to the equal ratios of the number of individuals per species noted in the community. On the other hand, community two is less even due to the presence of a more dominant species having an outlying value for abundance (70%) compared to the rest of other species. Areas that have a dominant species are generally considered to have less diversity than that of an even area. Community 1 and 2 have the same species richness but they have different species evenness. Species Dominance Species dominance refers to the relative importance of a species related to the degree of influence it has on ecosystem components. It shows how much more numerous the abundance of one species is relative to the abundance of the other species in an area. In order to measure species dominance, one must know the abundance of all species present in the ecosystem or community. The dominant species is the one that has the highest abundance value. Most of the time, the degree of dominance in the community is considered in order to measure the overall species diversity in an area. Species dominance can provide information that can be used to characterize communities based on habitat types and ecological sites. Moreover, this is useful in identifying ecosystem responses to climate change and the occurrence of diseases. Use the community two data presented earlier in the figure above as an example. Based on the figure, one can say that the species constituting 70% of the total number of trees in the community is the most dominant species. With this, ecologists can examine possible reasons for its dominance in the ecosystem and understand its role in sustaining the entire system. Cladistics Another way of seeing the degree of variation among species present in an ecosystem is through cladistics. Cladistics is a branch of taxonomy that deals with the categorization or classification of species based on their shared traits. Most of the time, cladistics is used to determine whether similar individuals belong to the same species or not. With this, statistics is important in establishing the species concept, where individuals are grouped into similar species based on their relatedness. Cladistic analysis was started in the 1960s by Willi Hennig, who is considered as the founder of phylogenetic systematics. This is where phylogenies of different groups are constructed using morphological and molecular data to visualize closeness between species. Cladogram Cladograms are diagrams that propose a hypothesis for the relatedness between species based on their shared characteristics. A cladogram may be based on molecular, anatomical, and genetic traits of species. With this, the resulting hypothesis represented by the cladogram may differ based on the cladistic data used to construct it. Cladogram vs Phylogenetic Tree One should be careful in differentiating cladograms from phylogenetic trees. Both trees reflect the relationships between species, but the two differ on how the length of the branches should be interpreted. Cladograms only reflect the topology or the pattern of branching that shows how organisms are related to a common ancestor based on their shared characteristics. On the other hand, phylogenetic trees involve evolutionary time together with the degree of changes that occurred in the species. With this, branch length in phylogenetic trees is calibrated based on evolutionary time, while branch length in cladogram does not pertain to anything and usually drawn in the same length. Cladogram Character States To fully understand a cladogram, one must know specific terminologies to describe characteristics based on their states (“character states”). The following are cladistic terms that are used to describe different character states in the cladogram: Plesiomorphy is an event where ancestral traits were retained in one or more taxa throughout evolution. In the cladogram, it is possible for two or more taxa to share plesiomorphic characters even if they cluster into different groups. Apomorphy is an event where derived characters were used to define specific clades in the cladogram. Most of the time, this allows the separation of one group to another due to the presence or absence of derived traits. Apomorphic characters can be classified as autapomorphic or synapomorphic: Autapomorphies happen when the derived trait is exhibited by a single species or group. Synapomorphies happen when all species in the entire clade possess the derived trait. Homoplasy refers to an event where a character is shared by at least two organisms but tends to be absent in common ancestors. Taxonomy is necessary because it helps us identify species that once lived, those living today, and those that have the chance to live in the future in a certain location. Also, our knowledge of taxonomy can help us understand the balance that exists within certain groups of organisms. Aside from being able to name, identify, and classify organisms, taxonomy can also help us understand biological diversity at a global level. With this knowledge, we can find ways to conserve and preserve organisms that are now in danger of extinction as a result of human activities. A classification is an important tool that has many uses. When you group things using your own set of criteria, you are performing the process of classification. Classifying things, not just organisms, help keep our daily life organized and more meaningful as we appreciate the importance of acknowledging even the simplest things to the most complex ones. Phylogeny is the study of the evolutionary development of groups of organisms. The relationships are hypothesized based on the idea that all life is derived from a common ancestor. Relationships among organisms are determined by shared characteristics, as indicated through genetic and anatomical comparisons. A phylogeny is represented in a diagram known as a phylogenetic tree. The branches of the tree represent ancestral and/or descendant lineages. Relatedness among taxa in a phylogenic tree is determined by descent from a recent common ancestor. Phylogeny is the evolutionary history of a group of related organisms. It is represented by a phylogenetic tree (left picture). One way of classifying organisms that shows phylogeny is by using the clade. A clade is a group of organisms that includes an ancestor and all of its descendants. Clades are based on cladistics. This is a method of comparing traits in related species to determine ancestor-descendant relationships. Clades are represented by cladograms (right picture). https://flexbooks.ck12.org/cbook/ck-12-biology-flexbook-2.0/section/5.11/primary/lesson/phylogenetic-classification-bio Phylogeny and taxonomy are two systems for classifying organisms in systematic biology. While the goal of phylogeny is to reconstruct the evolutionary tree of life, taxonomy uses a hierarchical format to classify, name, and identify organisms.
